Systems and methods of registration compensation in image guided surgery

ABSTRACT

A method performed by a computing system comprises receiving shape information for an elongate flexible portion of a medical instrument. The medical instrument includes a reference portion movably coupled to a fixture having a known pose in a surgical reference frame. The fixture includes a constraint structure having a known constraint structure location in the surgical reference frame. The elongate flexible portion is coupled to the reference portion and is sized to pass through the constraint structure. The method further includes receiving reference portion position information in the surgical reference frame; determining an estimated constraint structure location in the surgical reference frame from the reference portion position information and the shape information; determining a correction factor by comparing the estimated constraint structure location to the known constraint structure location; and modifying the shape information based upon the correction factor.

RELATED APPLICATIONS

This patent application is a continuation of U.S. application Ser. No.15/564,509, filed Oct. 5, 2017, which is the U.S. national phase ofInternational Application No. PCT/US2016/025891, filed Apr. 4, 2016,which designated the U.S. and claims priority to and the benefit of thefiling date of U.S. Provisional Patent Application No. 62/143,405,entitled “SYSTEMS AND METHODS OF REGISTRATION COMPENSATION IN IMAGEGUIDED SURGERY,” filed Apr. 6, 2015, all of which are incorporated byreference herein in their entirety.

FIELD

The present disclosure is directed to systems and methods for conductingan image guided procedure, and more particularly to systems and methodsfor compensating for errors in registration during an image guidedprocedure.

BACKGROUND

Minimally invasive medical techniques are intended to reduce the amountof tissue that is damaged during medical procedures, thereby reducingpatient recovery time, discomfort, and deleterious side effects. Suchminimally invasive techniques may be performed through natural orificesin a patient anatomy or through one or more surgical incisions. Throughthese natural orifices or incisions clinicians may insert minimallyinvasive medical instruments (including surgical, diagnostic,therapeutic, or biopsy instruments) to reach a target tissue location.To assist with reaching the target tissue location, the location andmovement of the medical instruments may be registered with pre-operativeor intra-operative images of the patient anatomy. With the image-guidedinstruments registered to the images, the instruments may navigatenatural or surgically created passageways in anatomical systems such asthe lungs, the colon, the intestines, the kidneys, the heart, thecirculatory system, or the like. Some image-guided instruments mayinclude a fiber-optic shape sensor which provides information about theshape of an elongated flexible instrument and about the pose of theinstrument's distal end. Systems and techniques for minimizing errorsassociated with registering the proximal end of the instrument to thepre-operative or intra-operative images are needed to maintain theaccuracy of pose estimations for the distal end of the instrument.

SUMMARY

The embodiments of the invention are summarized by the claims thatfollow the description.

In one embodiment, a method performed by a computing system comprisesreceiving shape information for an elongate flexible portion of amedical instrument. The medical instrument includes a reference portionmovably coupled to a fixture having a known pose in a surgical referenceframe. The fixture includes a constraint structure having a knownconstraint structure location in the surgical reference frame. Theelongate flexible portion is coupled to the reference portion and issized to pass through the constraint structure. The method furtherincludes receiving reference portion position information in thesurgical reference frame; determining an estimated constraint structurelocation in the surgical reference frame from the reference portionposition information and the shape information; determining a correctionfactor by comparing the estimated constraint structure location to theknown constraint structure location; and modifying the shape informationbased upon the correction factor.

In another embodiment, a method performed by a computing systemcomprises receiving, from a medical instrument, shape information forthe instrument. The medical instrument includes a reference portionmovably coupled to a fixture having a known pose in a surgical referenceframe. The fixture includes a constraint structure and an elongatedflexible portion coupled to the reference portion. The elongatedflexible portion is sized to pass through the constraint structure ofthe fixture at a known location in the surgical reference frame. Themethod further comprises receiving anatomical model information andregistering the instrument shape information to the anatomical modelinformation. Registering includes adjusting the instrument shapeinformation to pass through the known location in the surgical referenceframe.

It is to be understood that both the foregoing general description andthe following detailed description are exemplary and explanatory innature and are intended to provide an understanding of the presentdisclosure without limiting the scope of the present disclosure. In thatregard, additional aspects, features, and advantages of the presentdisclosure will be apparent to one skilled in the art from the followingdetailed description.

BRIEF DESCRIPTIONS OF THE DRAWINGS

Aspects of the present disclosure are best understood from the followingdetailed description when read with the accompanying figures. It isemphasized that, in accordance with the standard practice in theindustry, various features are not drawn to scale. In fact, thedimensions of the various features may be arbitrarily increased orreduced for clarity of discussion. In addition, the present disclosuremay repeat reference numerals and/or letters in the various examples.This repetition is for the purpose of simplicity and clarity and doesnot in itself dictate a relationship between the various embodimentsand/or configurations discussed.

FIG. 1 is a teleoperated medical system, in accordance with embodimentsof the present disclosure.

FIG. 2 illustrates a medical instrument system utilizing aspects of thepresent disclosure.

FIG. 3 illustrates a distal end of the medical instrument system of FIG.2 with an extended medical tool.

FIG. 4 is a flowchart illustrating a method used to provide guidance inan image guided surgical procedure according to an embodiment of thepresent disclosure.

FIG. 5 illustrates a registration display stage of a registrationtechnique according to an embodiment of the present disclosure.

FIG. 6 illustrates a side view of a surgical coordinate space includinga medical instrument mounted on an insertion assembly.

FIG. 7 a illustrates a portion of the insertion assembly of FIG. 6according to an alternative embodiment with a two degree of freedomconstraint structure mounted on the insertion assembly.

FIG. 7 b illustrates a cross-sectional view of the constraint structureof FIG. 7 a.

FIG. 8 a illustrates a portion of the insertion assembly of FIG. 6according to an alternative embodiment with a four degree of freedomconstraint structure mounted on the insertion assembly.

FIG. 8 b illustrates a cross-sectional view of the constraint structureof FIG. 8 a.

FIG. 9 a is a flowchart illustrating a method for correctingregistration of a medical instrument with a set of anatomical modelinformation.

FIG. 9 b is a flowchart illustrating a method for correcting the shapeinformation from a shape sensor.

FIG. 10 illustrates an initial registration of anatomical modelinformation to shape sensor information.

FIG. 11 illustrates a final registration corrected based on passage ofthe shape sensor through a constraint structure.

DETAILED DESCRIPTION

In the following detailed description of the aspects of the invention,numerous specific details are set forth in order to provide a thoroughunderstanding of the disclosed embodiments. However, it will be obviousto one skilled in the art that the embodiments of this disclosure may bepracticed without these specific details. In other instances well knownmethods, procedures, components, and circuits have not been described indetail so as not to unnecessarily obscure aspects of the embodiments ofthe invention. And, to avoid needless descriptive repetition, one ormore components or actions described in accordance with one illustrativeembodiment can be used or omitted as applicable from other illustrativeembodiments.

The embodiments below will describe various instruments and portions ofinstruments in terms of their state in three-dimensional space. As usedherein, the term “position” refers to the location of an object or aportion of an object in a three-dimensional space (e.g., three degreesof translational freedom along Cartesian X, Y, Z coordinates). As usedherein, the term “orientation” refers to the rotational placement of anobject or a portion of an object (three degrees of rotationalfreedom—e.g., roll, pitch, and yaw). As used herein, the term “pose”refers to the position of an object or a portion of an object in atleast one degree of translational freedom and to the orientation of thatobject or portion of the object in at least one degree of rotationalfreedom (up to six total degrees of freedom). As used herein, the term“shape” refers to a set of poses, positions, or orientations measuredalong an object.

Referring to FIG. 1 of the drawings, a teleoperated medical system foruse in, for example, surgical, diagnostic, therapeutic, or biopsyprocedures, is generally indicated by the reference numeral 100. Asshown in FIG. 1 , the teleoperated system 100 generally includes ateleoperational manipulator assembly 102 for operating a medicalinstrument 104 in performing various procedures on the patient P. Theassembly 102 is mounted to or near an operating table O. A masterassembly 106 allows the clinician or surgeon S to view theinterventional site and to control the slave manipulator assembly 102.

The master assembly 106 may be located at a surgeon's console which isusually located in the same room as operating table O. However, itshould be understood that the surgeon S can be located in a differentroom or a completely different building from the patient P. Masterassembly 106 generally includes one or more control devices forcontrolling the manipulator assemblies 102. The control devices mayinclude any number of a variety of input devices, such as joysticks,trackballs, data gloves, trigger-guns, hand-operated controllers, voicerecognition devices, body motion or presence sensors, or the like. Insome embodiments, the control devices will be provided with the samedegrees of freedom as the associated medical instruments 104 to providethe surgeon with telepresence, or the perception that the controldevices are integral with the instruments 104 so that the surgeon has astrong sense of directly controlling instruments 104. In otherembodiments, the control devices may have more or fewer degrees offreedom than the associated medical instruments 104 and still providethe surgeon with telepresence. In some embodiments, the control devicesare manual input devices which move with six degrees of freedom, andwhich may also include an actuatable handle for actuating instruments(for example, for closing grasping jaws, applying an electricalpotential to an electrode, delivering a medicinal treatment, or thelike).

The teleoperational assembly 102 supports the medical instrument system104 and may include a kinematic structure of one or more non-servocontrolled links (e.g., one or more links that may be manuallypositioned and locked in place, generally referred to as a set-upstructure) and a teleoperational manipulator. The teleoperationalassembly 102 includes a plurality of actuators or motors that driveinputs on the medical instrument system 104 in response to commands fromthe control system (e.g., a control system 112). The motors includedrive systems that when coupled to the medical instrument system 104 mayadvance the medical instrument into a naturally or surgically createdanatomical orifice. Other motorized drive systems may move the distalend of the medical instrument in multiple degrees of freedom, which mayinclude three degrees of linear motion (e.g., linear motion along the X,Y, Z Cartesian axes) and three degrees of rotational motion (e.g.,rotation about the X, Y, Z Cartesian axes). Additionally, the motors canbe used to actuate an articulable end effector of the instrument forgrasping tissue in the jaws of a biopsy device or the like. Motorposition sensors such as resolvers, encoders, potentiometers, and othermechanisms may provide sensor data to the teleoperational assemblydescribing the rotation and orientation of the motor shafts. Thisposition sensor data may be used to determine motion of the objectsmanipulated by the motors.

The teleoperational medical system 100 also includes a sensor system 108with one or more sub-systems for receiving information about theinstruments of the teleoperational assembly. Such sub-systems mayinclude a position sensor system (e.g., an electromagnetic (EM) sensorsystem); a shape sensor system for determining the position,orientation, speed, velocity, pose, and/or shape of the catheter tipand/or of one or more segments along a flexible body of instrumentsystem 104; an optical tracker system using cameras to monitor externaloptical markers on the instrument system and/or patient; and/or avisualization system for capturing images from the distal end of thecatheter system. One or more of these systems may be used to localizethe instrument relative to a frame of reference such as the patientframe of reference and/or the surgical environment frame of reference.

The visualization system (e.g., visualization system 231 of FIG. 2 ) mayinclude a viewing scope assembly that records a concurrent or real-timeimage of the surgical site and provides the image to the clinician orsurgeon S. The concurrent image may be, for example, a two or threedimensional image captured by an endoscope positioned within thesurgical site. In this embodiment, the visualization system includesendoscopic components that may be integrally or removably coupled to themedical instrument 104. However in alternative embodiments, a separateendoscope, attached to a separate manipulator assembly may be used withthe medical instrument to image the surgical site. The visualizationsystem may be implemented as hardware, firmware, software or acombination thereof which interact with or are otherwise executed by oneor more computer processors, which may include the processors of acontrol system 112 (described below).

The teleoperational medical system 100 also includes a display system110 for displaying an image or representation of the surgical site andmedical instrument system(s) 104 generated by sub-systems of the sensorsystem 108. The display 110 and the operator input system 106 may beoriented so the operator can control the medical instrument system 104and the operator input system 106 with the perception of telepresence.

The display system 110 may also display an image of the surgical siteand medical instruments captured by the visualization system. Thedisplay 110 and the control devices may be oriented such that therelative positions of the imaging device in the scope assembly and themedical instruments are similar to the relative positions of thesurgeon's eyes and hands so the operator can manipulate the medicalinstrument 104 and the hand control as if viewing the workspace insubstantially true presence. By true presence, it is meant that thepresentation of an image is a true perspective image simulating theviewpoint of an operator that is physically manipulating the instrument104.

Alternatively or additionally, the display 110 may present images of thesurgical site recorded pre-operatively or intra-operatively using imagedata from imaging technology such as, computed tomography (CT), magneticresonance imaging (MRI), fluoroscopy, thermography, ultrasound, opticalcoherence tomography (OCT), thermal imaging, impedance imaging, laserimaging, or nanotube X-ray imaging. The pre-operative or intra-operativeimage information may be presented as two-dimensional,three-dimensional, or four-dimensional (including e.g., time based orvelocity based information) images or as images from models created fromthe pre-operative or intra-operative image data sets.

In some embodiments often for purposes of image guided surgicalprocedures, the display 110 may display a virtual navigational image inwhich the actual location of the medical instrument 104 is registered(i.e., dynamically referenced) with the preoperative or concurrentimages/model to present the clinician or surgeon S with a virtual imageof the internal surgical site from the viewpoint of the location of thetip of the instrument 104. An image of the tip of the instrument 104 orother graphical or alphanumeric indicators may be superimposed on thevirtual image to assist the surgeon controlling the medical instrument.Alternatively, the instrument 104 may not be visible in the virtualimage.

In other embodiments, the display 110 may display a virtual navigationalimage in which the actual location of the medical instrument isregistered with preoperative or concurrent images to present theclinician or surgeon S with a virtual image of medical instrument withinthe surgical site from an external viewpoint. An image of a portion ofthe medical instrument or other graphical or alphanumeric indicators maybe superimposed on the virtual image to assist the surgeon controllingthe instrument 104.

The teleoperational medical system 100 also includes a control system112. The control system 112 includes at least one memory and at leastone computer processor (not shown), and typically a plurality ofprocessors, for effecting control between the medical instrument system104, the operator input system 106, the sensor system 108, and thedisplay system 110. The control system 112 also includes programmedinstructions (e.g., a computer-readable medium storing the instructions)to implement some or all of the methods described in accordance withaspects disclosed herein, including instructions for providingpathological information to the display system 110. While control system112 is shown as a single block in the simplified schematic of FIG. 1 ,the system may include two or more data processing circuits with oneportion of the processing optionally being performed on or adjacent theteleoperational assembly 102, another portion of the processing beingperformed at the operator input system 106, and the like. Any of a widevariety of centralized or distributed data processing architectures maybe employed. Similarly, the programmed instructions may be implementedas a number of separate programs or subroutines, or they may beintegrated into a number of other aspects of the teleoperational systemsdescribed herein. In one embodiment, control system 112 supportswireless communication protocols such as Bluetooth, IrDA, HomeRF, IEEE802.11, DECT, and Wireless Telemetry.

In some embodiments, control system 112 may include one or more servocontrollers that receive force and/or torque feedback from the medicalinstrument system 104. Responsive to the feedback, the servo controllerstransmit signals to the operator input system 106. The servocontroller(s) may also transmit signals instructing teleoperationalassembly 102 to move the medical instrument system(s) 104 which extendinto an internal surgical site within the patient body via openings inthe body. Any suitable conventional or specialized servo controller maybe used. A servo controller may be separate from, or integrated with,teleoperational assembly 102. In some embodiments, the servo controllerand teleoperational assembly are provided as part of a teleoperationalarm cart positioned adjacent to the patient's body.

The control system 112 may further include a virtual visualizationsystem to provide navigation assistance to the medical instrumentsystem(s) 104 when used in an image-guided surgical procedure. Virtualnavigation using the virtual visualization system is based uponreference to the acquired preoperative or intraoperative dataset of theanatomical passageways. More specifically, the virtual visualizationsystem processes images of the surgical site imaged using imagingtechnology such as computerized tomography (CT), magnetic resonanceimaging (MRI), fluoroscopy, thermography, ultrasound, optical coherencetomography (OCT), thermal imaging, impedance imaging, laser imaging,nanotube X-ray imaging, or the like. Software alone or in combinationwith manual input is used to convert the recorded images into segmentedtwo dimensional or three dimensional composite representation of apartial or an entire anatomical organ or anatomical region. An imagedata set is associated with the composite representation. The compositerepresentation and the image data set describe the various locations andshapes of the passageways and their connectivity. The images used togenerate the composite representation may be recorded preoperatively orintra-operatively during a clinical procedure. In an alternativeembodiment, a virtual visualization system may use standardrepresentations (i.e., not patient specific) or hybrids of a standardrepresentation and patient specific data. The composite representationand any virtual images generated by the composite representation mayrepresent the static posture of a deformable anatomic region during oneor more phases of motion (e.g., during an inspiration/expiration cycleof a lung).

During a virtual navigation procedure, the sensor system 108 may be usedto compute an approximate location of the instrument with respect to thepatient anatomy. The location can be used to produce both macro-level(external) tracking images of the patient anatomy and virtual internalimages of the patient anatomy. Various systems for using fiber opticsensors to register and display a medical implement together withpreoperatively recorded surgical images, such as those from a virtualvisualization system, are known. For example U.S. Pat. No. 8,900,131(filed May 13, 2011)(disclosing “Medical System Providing DynamicRegistration of a Model of an Anatomical Structure for Image-GuidedSurgery”) which is incorporated by reference herein in its entirety,discloses one such system.

The teleoperational medical system 100 may further include optionaloperation and support systems (not shown) such as illumination systems,steering control systems, irrigation systems, and/or suction systems. Inalternative embodiments, the teleoperational system may include morethan one teleoperational assembly and/or more than one operator inputsystem. The exact number of manipulator assemblies will depend on thesurgical procedure and the space constraints within the operating room,among other factors. The operator input systems may be collocated, orthey may be positioned in separate locations. Multiple operator inputsystems allow more than one operator to control one or more manipulatorassemblies in various combinations.

FIG. 2 illustrates a medical instrument system 200, which may be used asthe medical instrument system 104 in an image-guided medical procedureperformed with teleoperational medical system 100. Alternatively, themedical instrument system 200 may be used for non-teleoperationalexploratory procedures or in procedures involving traditional manuallyoperated medical instruments, such as endoscopy. Additionally oralternatively the medical instrument system 200 may be used to gather aset of data points corresponding to locations within patient anatomicpassageways.

The instrument system 200 includes a catheter system 202 coupled to aninstrument body 204. The catheter system 202 includes an elongatedflexible catheter body 216 having a proximal end 217 and a distal end ortip portion 218. In one embodiment, the flexible body 216 has anapproximately 3 mm outer diameter. Other flexible body outer diametersmay be larger or smaller. The catheter system 202 may optionally includea shape sensor 222 for determining the position, orientation, speed,velocity, pose, and/or shape of the catheter tip at distal end 218and/or of one or more segments 224 along the body 216. The entire lengthof the body 216, between the distal end 218 and the proximal end 217,may be effectively divided into the segments 224. If the instrumentsystem 200 is a medical instrument system 104 of a teleoperationalmedical system 100, the shape sensor 222 may be a component of thesensor system 108. If the instrument system 200 is manually operated orotherwise used for non-teleoperational procedures, the shape sensor 222may be coupled to a tracking system 230 that interrogates the shapesensor and processes the received shape data.

The shape sensor 222 may include an optical fiber aligned with theflexible catheter body 216 (e.g., provided within an interior channel(not shown) or mounted externally). In one embodiment, the optical fiberhas a diameter of approximately 200 μm. In other embodiments, thedimensions may be larger or smaller. The optical fiber of the shapesensor system 222 forms a fiber optic bend sensor for determining theshape of the catheter system 202. In one alternative, optical fibersincluding Fiber Bragg Gratings (FBGs) are used to provide strainmeasurements in structures in one or more dimensions. Various systemsand methods for monitoring the shape and relative position of an opticalfiber in three dimensions are described in U.S. Patent ApplicationPublication No. 2006/0013523 (filed Jul. 13, 2005) (disclosing “Fiberoptic position and shape sensing device and method relating thereto”);U.S. Pat. No. 7,772,541 (filed on Jul. 16, 2004) (disclosing“Fiber-optic shape and relative position sensing”); and U.S. Pat. No.6,389,187 (filed on Jun. 17, 1998) (disclosing “Optical Fibre BendSensor”), which are all incorporated by reference herein in theirentireties. Sensors in alternative embodiments may employ other suitablestrain sensing techniques, such as Rayleigh scattering, Ramanscattering, Brillouin scattering, and Fluorescence scattering. In otheralternative embodiments, the shape of the catheter may be determinedusing other techniques. For example, the history of the catheter'sdistal tip pose can be used to reconstruct the shape of the device overthe interval of time. As another example, historical pose, position, ororientation data may be stored for a known point of an instrument systemalong a cycle of alternating motion, such as breathing. This stored datamay be used to develop shape information about the catheter.Alternatively, a series of positional sensors, such as EM sensors,positioned along the catheter can be used for shape sensing.Alternatively, a history of data from a positional sensor, such as an EMsensor, on the instrument system during a procedure may be used torepresent the shape of the instrument, particularly if an anatomicalpassageway is generally static. Alternatively, a wireless device withposition or orientation controlled by an external magnetic field may beused for shape sensing. The history of the wireless device's positionmay be used to determine a shape for the navigated passageways.

The medical instrument system may, optionally, include a position sensorsystem 220. The position sensor system 220 may be a component of an EMsensor system with the sensor 220 including one or more conductive coilsthat may be subjected to an externally generated electromagnetic field.Each coil of the EM sensor system 220 then produces an inducedelectrical signal having characteristics that depend on the position andorientation of the coil relative to the externally generatedelectromagnetic field. In one embodiment, the EM sensor system may beconfigured and positioned to measure six degrees of freedom, e.g., threeposition coordinates X, Y, Z and three orientation angles indicatingpitch, yaw, and roll of a base point or five degrees of freedom, e.g.,three position coordinates X, Y, Z and two orientation angles indicatingpitch and yaw of a base point. Further description of an EM sensorsystem is provided in U.S. Pat. No. 6,380,732 (filed Aug. 11, 1999)(disclosing “Six-Degree of Freedom Tracking System Having a PassiveTransponder on the Object Being Tracked”), which is incorporated byreference herein in its entirety. In some embodiments, the shape sensormay also function as the position sensor because the shape of the sensortogether with information about the location of the base of the shapesensor (in the fixed coordinate system of the patient) allows thelocation of various points along the shape sensor, including the distaltip, to be calculated.

The medical instrument system may, optionally, include an opticaltracking system 227. The optical tracking system includes a plurality ofmarkers located on the instrument system 200. The markers may be locatedon the instrument body 204 external of the patient anatomy duringsurgical use or may be located on the catheter system 202 to be locatedinternally of the patient anatomy during surgical use. The markers maybe tracked during a surgical procedure by a stereoscopic camera system.

A tracking system 230 may include the position sensor system 220, theoptical tracking system 227, and/or the shape sensor system 222 todetermine the position, orientation, speed, pose, and/or shape of thedistal end 218 and of one or more segments 224 along the instrument 200.The tracking system 230 may be implemented as hardware, firmware,software or a combination thereof which interact with or are otherwiseexecuted by one or more computer processors, which may include theprocessors of a control system 112.

The flexible catheter body 216 includes a channel 221 sized and shapedto receive a medical instrument 226. Medical instruments may include,for example, image capture probes, biopsy instruments, laser ablationfibers, or other surgical, diagnostic, or therapeutic tools. Medicaltools may include end effectors having a single working member such as ascalpel, a blunt blade, an optical fiber, or an electrode. Other endeffectors may include, for example, forceps, graspers, scissors, or clipappliers. Examples of electrically activated end effectors includeelectrosurgical electrodes, transducers, sensors, and the like. Invarious embodiments, the medical tool 226 may be an image capture probe(e.g., a component of visualization system 231) that includes astereoscopic or monoscopic camera at or near the distal end 218 of theflexible catheter body 216 for capturing images (including video images)that are processed for display. The image capture probe may include acable coupled to the camera for transmitting the captured image data.Alternatively, the image capture instrument may be a fiber-optic bundle,such as a fiberscope, that couples to the visualization system. Theimage capture instrument may be single or multi-spectral, for examplecapturing image data in one or more of the visible, infrared, orultraviolet spectrums.

The medical instrument 226 may house cables, linkages, or otheractuation controls (not shown) that extend between the proximal anddistal ends of the instrument to controllably bend the distal end of theinstrument. Steerable instruments are described in detail in U.S. Pat.No. 7,316,681 (filed on Oct. 4, 2005) (disclosing “Articulated SurgicalInstrument for Performing Minimally Invasive Surgery with EnhancedDexterity and Sensitivity”) and U.S. Pat. No. 9,259,274 (filed Sep. 30,2008) (disclosing “Passive Preload and Capstan Drive for SurgicalInstruments”), which are incorporated by reference herein in theirentireties.

The flexible catheter body 216 may also houses cables, linkages, orother steering controls (not shown) that extend between the housing 204and the distal end 218 to controllably bend the distal end 218 as shown,for example, by the broken dashed line depictions 219 of the distal end.Steerable catheters are described in detail in U.S. Pat. No. 9,452,276(filed Oct. 14, 2011) (disclosing “Catheter with Removable VisionProbe”), which is incorporated by reference herein in its entirety. Inembodiments in which the instrument system 200 is actuated by ateleoperational assembly, the housing 204 may include drive inputs thatremovably couple to and receive power from motorized drive elements ofthe teleoperational assembly. In embodiments in which the instrumentsystem 200 is manually operated, the housing 204 may include grippingfeatures, manual actuators, or other components for manually controllingthe motion of the instrument system. The catheter system may besteerable or, alternatively, the system may be non-steerable with nointegrated mechanism for operator control of the instrument bending.Also or alternatively, one or more lumens, through which medicalinstruments can be deployed and used at a target surgical location, aredefined in the walls of the flexible body 216.

In various embodiments, the medical instrument system 200 may include aflexible bronchial instrument, such as a bronchoscope or bronchialcatheter, for use in examination, diagnosis, biopsy, or treatment of alung. The system 200 is also suited for navigation and treatment ofother tissues, via natural or surgically created connected passageways,in any of a variety of anatomical systems, including the colon, theintestines, the kidneys, the brain, the heart, the circulatory system,and the like.

The information from the tracking system 230 may be sent to a navigationsystem 232 where it is combined with information from the visualizationsystem 231 and/or the preoperatively obtained models to provide thesurgeon or other operator with real-time position information on thedisplay system 110 for use in the control of the instrument 200. Thecontrol system 112 may utilize the position information as feedback forpositioning the instrument 200. Various systems for using fiber opticsensors to register and display a surgical instrument with surgicalimages are provided in U.S. Pat. No. 8,900,131, filed May 13, 2011,disclosing, “Medical System Providing Dynamic Registration of a Model ofan Anatomical Structure for Image-Guided Surgery,” which is incorporatedby reference herein in its entirety.

In the embodiment of FIG. 2 , the instrument 200 is teleoperated withinthe teleoperational medical system 100. In an alternative embodiment,the teleoperational assembly 102 may be replaced by direct operatorcontrol. In the direct operation alternative, various handles andoperator interfaces may be included for hand-held operation of theinstrument.

In alternative embodiments, the teleoperated system may include morethan one slave manipulator assembly and/or more than one masterassembly. The exact number of manipulator assemblies will depend on themedical procedure and the space constraints within the operating room,among other factors. The master assemblies may be collocated, or theymay be positioned in separate locations. Multiple master assembliesallow more than one operator to control one or more slave manipulatorassemblies in various combinations.

As shown in greater detail in FIG. 3 , medical tool(s) 228 for suchprocedures as surgery, biopsy, ablation, illumination, irrigation, orsuction can be deployed through the channel 221 of the flexible body 216and used at a target location within the anatomy. If, for example, thetool 228 is a biopsy instrument, it may be used to remove sample tissueor a sampling of cells from a target anatomical location. The medicaltool 228 may be used with an image capture probe also within theflexible body 216. Alternatively, the tool 228 may itself be the imagecapture probe. The tool 228 may be advanced from the opening of thechannel 221 to perform the procedure and then retracted back into thechannel when the procedure is complete. The medical tool 228 may beremoved from the proximal end 217 of the catheter flexible body or fromanother optional instrument port (not shown) along the flexible body.

FIG. 4 is a flowchart illustrating a general method 450 for use inconducting an image guided surgical procedure. At a process 452,pre-operative or intra-operative image data is obtained from imagingtechnology such as, computed tomography (CT), magnetic resonance imaging(MRI), fluoroscopy, thermography, ultrasound, optical coherencetomography (OCT), thermal imaging, impedance imaging, laser imaging, ornanotube X-ray imaging. The pre-operative or intra-operative image datamay correspond to two-dimensional, three-dimensional, orfour-dimensional (including e.g., time based or velocity basedinformation) images. At a process 454, computer software alone or incombination with manual input is used to convert the recorded imagesinto a segmented two dimensional or three dimensional compositerepresentation or model of a partial or an entire anatomical organ oranatomical region. The composite representation and the image data setdescribe the various locations and shapes of the passageways and theirconnectivity. More specifically, during the segmentation process theimages are partitioned into segments or elements (e.g., pixels orvoxels) that share certain characteristics or computed properties suchas color, density, intensity, and texture. This segmentation processresults in a two- or three-dimensional reconstruction that forms a modelof the target anatomy based on the obtained image. To represent themodel, the segmentation process may delineate sets of voxelsrepresenting the target anatomy and then apply a function, such asmarching cube function, to obtain a 3D surface that encloses the voxels.Additionally or alternatively, the model may include a centerline modelthat includes a set of interconnected lines segments or points extendingthrough the centers of the modeled passageways. At a process 456, theanatomical model data is registered to the patient anatomy prior toand/or during the course of an image-guided surgical procedure on thepatient. Generally, registration involves the matching of measured pointto points of the model through the use of rigid and/or non-rigidtransforms. Measured points may be generated using, for example,landmarks in the anatomy, optical markers, and/or electromagnetic coilsscanned during the image and tracked during the procedure. Additionallyor alternatively, measured points may be generated using shape sensorinformation and an iterative closest point (ICP) technique.

FIG. 5 illustrates a display system 500 displaying a rendering ofanatomical passageways 502 of a human lung 504 based upon anatomicalmodel information. With the surgical environment frame of referenceregistered to the model frame of reference, the current shape of thecatheter 510 and the location of the distal end 518 may be located anddisplayed concurrently with the rendering of the model passageways 502.The movement of the catheter 510 is tracked and displayed as thecatheter moves within the passageways 502, providing guidance to theuser controlling the movement of the catheter.

As described above, various localization systems may be used to localizeinstruments to the surgical frame of reference (which is the same orapproximately the same as the patient frame of reference for astationary patient) during an image guided surgical procedure. Suchlocalization systems include the use of EM sensors, impedance basedsensors, ultrasound based sensors, fiber optic based sensors, and/oroptical tracker based sensors. These sensors may be located on thecomponents of the instrument that are located within the patient anatomyduring a medical procedure or may be located on the components of theinstrument that remain external of the patient anatomy during a medicalprocedure. Some of the localization systems have characteristics thatmay limit their utility for localizing instruments in a surgicalenvironment. For example, with EM or impedance based sensing, metallicobjects or certain electronic devices used in the surgical environmentmay create disturbances that impair the quality of the sensed data. Withoptical tracker based systems, tracking camera systems may be too largefor observation of markers within the anatomy or may obstruct theclinical workflow if observing markers external to the anatomy.

Fiber optic shape sensors are particularly useful as localizationsensors because they provide data about the entire shape of theinstrument, including the pose of the distal tip, without beingsensitive to metal objects in the area or requiring obstructive imagingequipment. When using fiber optic shape sensors, however, small positionand orientation errors at the proximal end of the optical fiber maygenerate large accumulated position and orientation errors for thedistal end of the sensor due to the length of the sensor (e.g.,approximately one meter). Systems and methods to correct for theseerrors are described below and may be used to generate more accurateregistrations of the optical fiber to the anatomic model information.

FIG. 6 illustrates a surgical environment 600, with a surgicalcoordinate system X_(S), Y_(S), Z_(S), in which a patient P ispositioned on a platform 602. The patient P may be stationary within thesurgical environment in the sense that gross patient movement is limitedby sedation, restraint, or other means. Thus, the patient frame ofreference may be considered to be the same as or fixed with respect tothe surgical environment frame of reference. Cyclic anatomical motionincluding respiration and cardiac motion of the patient P will continue.Within the surgical environment 600, a medical instrument 604 is coupledto an instrument carriage 606. The instrument carriage 606 is mounted toan insertion stage 608. The insertion stage 608 may itself be fixedwithin the surgical environment 600. Alternatively, the insertion stagemay be coupled to a manipulator arm of a teleoperational system.Movement of the manipulator arm and thus the insertion stage may betracked within the surgical environment 600 using, for example,kinematic-based joint sensors, optical tracking, EM-tracking, or otherknown tracking systems for the manipulator arm. Thus, the location ofthe insertion stage in the environment may be known even if theinsertion stage itself is not fixed. The insertion stage may be a linearstage as shown in the present embodiment or may have anotherpredetermined and known shape in the surgical environment.

The instrument carriage 606 may be a component of a teleoperationalmanipulator assembly (e.g., assembly 102) that couples to the instrument604 to control insertion motion (i.e. motion in an X_(S) direction) and,optionally, motion of a distal end of the instrument in multipledirections including yaw, pitch, and roll. The instrument carriage 606or the insertion stage 608 may include servomotors (not shown) thatcontrol motion of the instrument carriage along the insertion stage.

The medical instrument 604 may include a flexible catheter 610 coupledto a proximal rigid instrument body 612. The rigid instrument body 612is coupled and fixed relative to the instrument carriage 606 and thus ismovably coupled to the insertion stage 608 via the carriage. An opticalfiber shape sensor 614 is fixed at a reference portion 616 of the rigidinstrument body 612. In an alternative embodiment, the reference portion616 of the sensor 614 may be movable along the body 612 but the locationof the reference portion may be known (e.g., via a tracking sensor orother tracking device). A frame of reference for the reference portion616 has a coordinate system X_(T), Y_(T), Z_(T). The shape sensor 614measures a shape from the reference portion 616 to another point such asthe distal end 618 of the catheter 610. The medical instrument 604 maybe substantially similar to the medical instrument system 200.

A position measuring device 620 provides information about the positionof the rigid instrument body 612 as it moves on the insertion stage 608along an insertion axis A. The position measuring device 620 may includeresolvers, encoders, potentiometers, and other mechanisms that determinethe rotation and orientation of the motor shafts controlling the motionof the instrument carriage 606 and consequently provides indirectmeasurement of the motion of the rigidly attached instrument body 612.Alternatively, the position measuring device 620 may directly measurethe motion of the instrument body 612 using, for example, a mechanicaltape measure, a laser distance sensor, or electromagnetic or opticaltrackers. In this embodiment, the insertion stage 608 is linear, but inalternative embodiments it may be curved or have a combination of curvedand linear sections. Optionally, the linear track may be collapsible asdescribed, for example, in U.S. Provisional Patent Application No.62/029,917 (filed Jul. 28, 2014)(disclosing “Guide Apparatus ForDelivery Of A Flexible Instrument And Methods Of Use”) which isincorporated by reference herein in its entirety. FIG. 6 shows theinstrument body 612 and carriage 606 in a retracted position along theinsertion stage 608. In this retracted position, the reference portion616 is at a position L₀ on the axis A. In this position along theinsertion stage 608, an X_(S) component of the location of the referenceportion 616 may be set to a zero or original value. With this retractedposition of the instrument body 612 and carriage 606, the distal end 618of the catheter may be positioned just inside an entry orifice of thepatient P.

As shown in FIG. 6 , a constraint structure 622 is rigidly coupled tothe insertion stage 608. In an alternative embodiment, the constraintstructure may be movable but the location of the constraint structuremay be known (e.g., via a tracking sensor or other tracking device) inthe surgical reference frame. Because the location of the constraintstructure 622 is fixed or known in the surgical coordinate system 600,the portion of the catheter 610 passing through the constraint structure622 also passes through the same fixed or known location. Thisinformation about the fixed or known location of the constraintstructure can be used to determine or correct the orientation of theshape information from the sensor 614 in the surgical coordinate systemand thus also generate a more accurate estimate of the location of thedistal end of the sensor and catheter.

As shown in FIG. 7 a , a constraint structure 622 a may be a ring shapedmember sized to receive the catheter 610 in sliding passage, along theaxis A, and having a short length L1, in a +X_(S), −X_(S) direction, toconstrain movement of the catheter in two degrees of freedom. In oneembodiment, the ring has a length L1 of approximately 2 mm. Otherrelatively short lengths that constrain translation in the Y_(S) andZ_(S) directions while permitting pivoting motion about the constrainedpoint may be suitable. As shown in FIG. 7 b , the catheter 610 isconstrained in that it must pass through the ring constraint structure622 a, and hence the Y_(S) and Z_(S) coordinates of one point of thecatheter are constrained to equal the Y_(S) and Z_(S) coordinates of thecenter of the constraint structure. In other words, at the location ofthe constraint structure 622 a, translational movement of the catheter610 is restricted in the +/−Y_(S) and +/−Z_(S) directions. Since thelength L1 is relatively short, the section of the shaft passing throughthe constraint structure 622 a, is not constrained in orientation andmay still pivot around the constrained point. Alternatively, as shown inFIG. 8 a , a constraint structure 622 b may be a tube shaped membersized to receive the catheter 610 in sliding passage, in a +X_(S),−X_(S) direction, and having a length L2, longer than L1, to constrainmovement of the catheter in four degrees of freedom. In one embodiment,the tube shaped member has a length L2 of approximately 2 cm. Otherlengths that constrain translation degrees of freedom in the Y_(S) andZ_(S) directions and rotational degrees of freedom in the pitch and yawdirections may be suitable. As shown in FIG. 8 b , the constraintstructure 622 b constrains a section of the shaft of the catheter insuch a way that not only are the Y_(S) and Z_(S) coordinates of thatsection constrained to equal the Y_(S) and Z_(S) coordinates of thecenterline of the constraint structure, but also the pitch and yaworientation angles are constrained to align with the X_(S) direction.The two position and two orientation constraints add up to theconstraint structure constraining four degrees of freedom.

FIG. 9 a is a flowchart illustrating a method 700 used to provideguidance to a clinician in an image guided surgical procedure on thepatient P in the surgical environment 600, according to an embodiment ofthe present disclosure. At a process 702, shape information is receivedfrom the optical fiber shape sensor 614 extending within the instrument604. The shape information describes the shape of the instrument 604between the proximal reference portion 616 and the distal end 618. Theaccumulated shape information also describes the position andorientation of the distal end 618 relative to the proximal referenceportion 616 (i.e., in the X_(T), Y_(T), Z_(T) coordinate frame). Shapeinformation 800 from the sensor 614 may be illustrated as shown in inFIG. 10 . The shape information also provides information about thelocation of the constraint relative to the proximal reference portion616. As the shape sensor is moved along the axis A, the observed shapeinformation from the location of the fixed or known constraint will bethe same (i.e. will exhibit the same known constraints) for differentlocations of the proximal reference portion 616.

At a process 704, anatomical model information is received. As describedabove, the anatomical model information may be generated frompre-operative or intra-operative image data obtained from imagingtechnology including CT, MRI, and/or fluoroscopy. The pre-operative orintra-operative image data may correspond to two-dimensional,three-dimensional, or four-dimensional images. A segmentation processgenerates a two- or three-dimensional reconstruction that forms a modelof the anatomy based on the obtained images. The model may, for example,be represented as a centerline model that includes a set ofinterconnected line segments or points extending through the centers ofthe modeled passageways or may be represented as a surface model thatdescribes the surfaces of the modeled passageways. FIG. 10 illustratesanatomical model information 802 that represents a centerline model of aset of anatomic passageways.

At a process 706, the instrument shape information 800 is registered tothe anatomical model information 802. To perform the registrationbetween the shape information and the anatomical model information, bothsets of information are registered to the surgical frame of reference(which is the same as the patient frame of reference for a stationarypatient). The proximal reference portion 616 of the sensor 614 is fixedor known relative to the rigid instrument body 612 which is coupled tothe instrument carriage 606. The instrument carriage moves along theinsertion stage 608 which has a fixed or known location in the surgicalreference frame. By tracking the movement of the instrument carriageusing for example, sensor 620, the position and orientation of theproximal reference portion 616, and therefore the proximal referenceportion frame of reference, relative to the surgical reference frame canbe determined and tracked.

Registering the anatomic model information 802 to the surgical referenceframe may be performed according to any of various methods. For example,registration may be accomplished using a marker 624 affixed to thepatient during pre-operative or intra-operative imaging that remains onthe patient during the surgical procedure and a marker 626 affixed tothe instrument at the reference portion 616 of the sensor 614. In oneembodiment, the marker 624 may be an optical tracker having adistinctive configuration of two or three dimensional markings. Anotheroptical tracker may be positioned on the reference portion 616 of thesensor 614. Registration based on optical tracking is described in U.S.Pat. App. Pub. No. 2018/0256262, which is incorporated by referenceherein in its entirety. In another embodiment, the markers 624, 626 maybe EM sensors. Registration based on EM sensors is described, forexample, in U.S. Pat. No. 10,555,775 (filed May 16, 2005)(disclosing“Methods and system for performing 3-D tool tracking by fusion of sensorand/or camera derived data during minimally invasive robotic surgery”)which is incorporated by reference herein in its entirety. Other methodsfor registration include the use of a registration algorithm based onanatomical points gathered by the shape sensor and are described in U.S.Pat. App. Pub. No. 2018/0153621 which is incorporated by referenceherein in its entirety. After this registration, the proximal referenceportion, the anatomical model information, and the location of theconstraint structure are known in the surgical reference frame. Thus,the shape information and anatomical model information are registered toeach other in the surgical reference frame.

As shown in FIG. 10 , the initial registration of the instrument shapeinformation 800 to the anatomical model information 802 may be faultydue to errors associated with the registered orientation of the shapesensor proximal reference portion frame of reference to the model frameof reference. Small errors associated with the position and/ororientation of the reference portion frame of reference relative may becompounded and magnified when they form the basis for determining thepose of the distal end 804 of the sensor. Thus, as shown in FIG. 10 , asmall orientation error with the proximal reference portion 616 of shapeinformation 800 may generate significant error in locating the distalend 804 of the shape sensor. These errors may be significant in thatthey locate the distal end 804 of the shape sensor in the wronganatomical passageway.

At a process 708, the instrument shape information 800 is corrected bycompensating for errors associated with the orientation or position ofthe sensor reference portion frame of reference. The constraintstructure 622 provides a known location in the surgical frame ofreference through which the instrument must pass. Thus, the shape sensorinformation 800 must pass through the known location with the degree offreedom constraints enforced by the constraint structure 622. An initialregistration that does not observe the known constraints imposed by theconstraint structure may be corrected by rotating the orientation and/ortranslating the position of the shape sensor information 800 to passthrough the known location with the known pose dictated by theconstraint structure 622. As shown in FIG. 11 , the orientation of theshape information 800 has been adjusted to route the shape information800 through the location of the constraint structure 622.

FIG. 9 b is a flowchart illustrating a method 710 for correcting theshape information from a shape sensor. At a process 712, shapeinformation is received from the optical fiber shape sensor 614extending within the instrument 604. The shape information describes theshape of the instrument 604 between the proximal reference portion 616and the distal end 618. The accumulated shape information also describesthe position and orientation of the distal end 618 relative to theproximal reference portion 616 (i.e., in the X_(T), Y_(T), Z_(T)coordinate frame). The shape information also provides information aboutthe location of the constraint relative to the proximal referenceportion 616. As the shape sensor is moved along the axis A, the shapeinformation at the location of the fixed or known constraint will be thesame for different locations of the proximal reference portion.

At a process 714, proximal reference portion 616 position information inthe surgical reference frame is received or determined. In oneembodiment, a calibration procedure is performed to calibrate a relativeposition and/or orientation of the proximal reference portion 616 alongan insertion path. For example, the position and orientation of theportion 616 is measured as the carriage 606 moves from a retractedposition with the portion 616 at location L₀ to an advanced positionwith the portion 616 at the location L₁. The calibration proceduredetermines the direction of the movement of the portion 616 for eachchange in the position measuring device 620. In this embodiment, wherethe insertion stage 608 restricts movement of the carriage 606 to alinear path, the calibration procedure determines the direction of thestraight line. From the slope of the insertion stage track, the positionand orientation of the portion 616 in the surgical environment 600 maybe determined for every corresponding measurement of the positionmeasuring device 620. In an alternative embodiment, if the insertionstage has a curved or otherwise non-linear shape, the calibrationprocedure may determine the non-linear shape so that for everymeasurement of the position device, the position and orientation of theportion 616 in the surgical environment may be determined. For example,the distal tip of the catheter may be held in a fixed position while theinstrument body is routed along the non-linear insertion stage. Theposition and orientation data collected by the shape sensor from theportion 616 is correlated with the position measuring device data as theinstrument body is routed along the insertion stage, thus calibratingmovement of the portion 616 along the axis A of the insertion stage 608.

At a process 716, the position and orientation of the constraintstructure 622 in the surgical reference frame may be predicted basedupon the instrument shape information and the proximal reference portion616 position information. More specifically, for any given measurementof the position measuring device 620, the position of the proximalreference portion 616 is known in the surgical reference frame basedupon the calibration. From the shape information, the position andorientation of the constraint structure 622 relative to the referenceportion 616 is also known. Thus, for each position of the referenceportion 616, the position and orientation of the constraint structure622 in the surgical reference frame may be predicted by combining thecalibrated insertion position information and the shape information.

At a process 718, the predicted position and orientation of theconstraint structure 622 in the surgical reference frame is compared tothe known position and orientation of the constraint structure 622 inthe surgical reference frame. A correction factor including position andorientation components between the predicted and known locations of theconstraint structure is determined. This correction factor is applied tothe shape sensor information to correct the position and orientation ofthe distal end of the shape sensor information in the surgical referenceframe. Optionally, this corrected shape sensor information may be usedfor registration with anatomic model information to perform an imageguided surgical procedure. Optionally, the localized instrument may bedisplayed with the anatomic model to assist the clinician in an imageguided surgery.

Although the systems and methods of this disclosure have been describedfor use in the connected bronchial passageways of the lung, they arealso suited for navigation and treatment of other tissues, via naturalor surgically created connected passageways, in any of a variety ofanatomical systems including the colon, the intestines, the kidneys, thebrain, the heart, the circulatory system, or the like.

One or more elements in embodiments of the invention may be implementedin software to execute on a processor of a computer system such ascontrol system 112. When implemented in software, the elements of theembodiments of the invention are essentially the code segments toperform the necessary tasks. The program or code segments can be storedin a processor readable storage medium or device that may have beendownloaded by way of a computer data signal embodied in a carrier waveover a transmission medium or a communication link. The processorreadable storage device may include any medium that can storeinformation including an optical medium, semiconductor medium, andmagnetic medium. Processor readable storage device examples include anelectronic circuit; a semiconductor device, a semiconductor memorydevice, a read only memory (ROM), a flash memory, an erasableprogrammable read only memory (EPROM); a floppy diskette, a CD-ROM, anoptical disk, a hard disk, or other storage device, The code segmentsmay be downloaded via computer networks such as the Internet, Intranet,etc.

Note that the processes and displays presented may not inherently berelated to any particular computer or other apparatus. The requiredstructure for a variety of these systems will appear as elements in theclaims. In addition, the embodiments of the invention are not describedwith reference to any particular programming language. It will beappreciated that a variety of programming languages may be used toimplement the teachings of the invention as described herein.

While certain exemplary embodiments of the invention have been describedand shown in the accompanying drawings, it is to be understood that suchembodiments are merely illustrative of and not restrictive on the broadinvention, and that the embodiments of the invention not be limited tothe specific constructions and arrangements shown and described, sincevarious other modifications may occur to those ordinarily skilled in theart.

1-28. (canceled)
 29. A system comprising: a fixture having a knownlocation in a surgical reference frame, the fixture including aconstraint structure having a known constraint structure pose in thesurgical reference frame; a medical instrument including: a referenceportion movably coupled to the fixture; an elongate flexible portioncoupled to the reference portion, wherein the elongate flexible portionis sized to pass through the constraint structure; and a shape sensorextending within the medical instrument; a position measuring devicethat measures motion of the reference portion with respect to thefixture as the reference portion moves along the fixture; and acomputing system configured to: receive shape information for themedical instrument from the shape sensor; receive reference portionposition information in the surgical reference frame from the positionmeasuring device; determine an estimated constraint structure pose inthe surgical reference frame from the reference portion positioninformation and the shape information; determine a correction factor bycomparing the estimated constraint structure pose to the knownconstraint structure pose; and modify the shape information based uponthe correction factor.
 30. The system of claim 29, wherein the shapesensor is a fiber optic shape sensor.
 31. The system of claim 29,wherein the fixture restricts the motion of the reference portion alonga linear path or a curved path.
 32. The system of claim 29, wherein theconstraint structure is at a fixed location relative to the fixture. 33.The system of claim 29, further comprising a tracking sensor configuredto track the known constraint structure pose, wherein the constraintstructure is moveable relative to the fixture.
 34. The system of claim29, wherein the position measuring device comprises a motor positionsensor configured to determine a rotation or an orientation of a motorshaft controlling the motion of the reference portion as the referenceportion moves along an insertion axis of the fixture.
 35. The system ofclaim 34, wherein the motor position sensor comprises a resolver, anencoder, or a potentiometer.
 36. The system of claim 29, wherein theposition measuring device comprises a direct measurement device.
 37. Thesystem of claim 36, wherein the direct measurement device comprises amechanical tape measure, a laser distance sensor, an electromagnetictracker, or an optical tracker.
 38. The system of claim 29, furthercomprising a teleoperated manipulator fixed in the surgical referenceframe, wherein the fixture is a component of the teleoperatedmanipulator.
 39. The system of claim 38, wherein the constraintstructure has a fixed position with respect to the fixture.
 40. Thesystem of claim 39, wherein the constraint structure is configured topermit pivoting motion of the elongate flexible portion about the fixedposition.
 41. A method performed by a computing system, comprising:receiving shape information for an elongate flexible portion of amedical instrument, the medical instrument including a reference portionand the elongate flexible portion coupled to the reference portion,wherein the reference portion is movably coupled to a fixture having aknown location in a surgical reference frame, the fixture including aconstraint structure having a known constraint structure pose in thesurgical reference frame, wherein the elongate flexible portion is sizedto pass through the constraint structure; receiving reference portionposition information in the surgical reference frame from a positionmeasuring device that measures motion of the reference portion withrespect to the known location in the surgical reference frame as thereference portion moves along the fixture; determining an estimatedconstraint structure pose in the surgical reference frame from thereference portion position information and the shape information;determining a correction factor by comparing the estimated constraintstructure pose to the known constraint structure pose; and modifying theshape information based upon the correction factor.
 42. The method ofclaim 41, further comprising calibrating a relative reference portionposition or a reference portion orientation including correlating theshape information with the reference portion position information fromthe position measuring device.
 43. The method of claim 42, wherein thecalibrating includes determining a direction of the motion of thereference portion as the reference portion moves along the fixture. 44.The method of claim 41, further comprising correcting a position andorientation of a distal tip based on the modified shape information,wherein the distal tip is at a distal end of the elongate flexibleportion.
 45. The method of claim 41, wherein the shape information isfiber optic shape sensor data.
 46. The method of claim 41, wherein thefixture is a component of a teleoperated manipulator fixed in thesurgical reference frame.
 47. The method of claim 46, wherein theconstraint structure has a fixed position with respect to the fixture.48. The method of claim 47, wherein the constraint structure permitspivoting motion of the elongate flexible portion about the fixedposition.